{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"submitter":["Le MT"],"pubmed_abstract":["Two-dimensional tandem mass spectrometry (2D MS/MS) provides in-depth biopolymer structural information previously not directly accessible with traditional one-dimensional MS/MS workflows, and in significantly less time (<1 second per sample). In this study, we enhance 2D MS/MS data analysis for greater applicability in omics workflows and address challenges in sequencing peptides in mixtures. We designed a graph-theory-based framework to efficiently manage, visualize, and maximize the structural information extractable from 2D MS/MS spectra. Graph analysis algorithms, including a PageRank-based method, are shown to deconvolve MS/MS signals and group together product ions from the same presursor peptide, enabling the reconstruction of peptide fragmentation trees. From this, MS <sup><i>n</i"],"journal":["Chemical science"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12418246"],"repository":["biostudies-literature"],"pubmed_title":["Framework for &lt;i&gt;de novo&lt;/i&gt; sequencing of peptide mixtures &lt;i&gt;via&lt;/i&gt; network analysis and two-dimensional tandem mass spectrometry."],"pmcid":["PMC12418246"],"pubmed_authors":["Holden DT","Le MT","Zhu Y","Gleich DF","Cooks RG","Dziekonski ET"],"additional_accession":[]},"is_claimable":false,"name":"Framework for &lt;i&gt;de novo&lt;/i&gt; sequencing of peptide mixtures &lt;i&gt;via&lt;/i&gt; network analysis and two-dimensional tandem mass spectrometry.","description":"Two-dimensional tandem mass spectrometry (2D MS/MS) provides in-depth biopolymer structural information previously not directly accessible with traditional one-dimensional MS/MS workflows, and in significantly less time (<1 second per sample). In this study, we enhance 2D MS/MS data analysis for greater applicability in omics workflows and address challenges in sequencing peptides in mixtures. We designed a graph-theory-based framework to efficiently manage, visualize, and maximize the structural information extractable from 2D MS/MS spectra. Graph analysis algorithms, including a PageRank-based method, are shown to deconvolve MS/MS signals and group together product ions from the same presursor peptide, enabling the reconstruction of peptide fragmentation trees. From this, MS <sup><i>n</i","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 Sep","modification":"2026-06-02T00:24:09.017Z","creation":"2026-05-24T03:07:16.605Z"},"accession":"S-EPMC12418246","cross_references":{"pubmed":["40933073"],"doi":["10.1039/d5sc03762j"]}}